Boosting Long-Range Surface-Enhanced Raman Scattering on Plasmonic Nanohole Arrays for Ultrasensitive Detection of MiRNA

Ultrasensitive upconverting nanoprobes for in situ imaging of drug-induced liver injury using miR-122 as the biomarker

Drug-induced liver injury (DILI) is a frequent adverse drug reaction. The current clinical diagnostic methods are inadequate for accurate and early detection of DILI due to the lack of effective diagnostic biomarkers. Hepatocyte-specific miR-122 is released from injured hepatocytes promptly and its efflux is significantly correlated with the progression of DILI. Therefore, achieving precise in situ detection of miR-122 with high sensitivity is vital for early visualization of DILI. Herein, a new nanoprobe, consisting of miR-122 aptamer, upconversion nanoparticles (UCNPs) and Prussian blue nanoparticles (PBNPs) was introduced for the early and sensitive detection of DILI in situ. As the nanoprobes reached in the liver, miR-122 aptamer-based entropy-driven strand displacement (ESDR) signal amplification reaction was triggered and luminescence resonance energy transfer (LRET) between UCNPs and PBNPs was responded to achieve the high-fidelity detection of DILI. A negative correlation was observed between the intensity of upconversion luminescence (UCL) and the concentration of miR-122. UCL imaging conducted both in vivo and ex vivo indicated that a reduction in miR-122 concentration led to an increase in UCL intensity, revealing a precise state of DILI. The detection technique demonstrated a positive correlation between signal intensity and severity, offering a more straightforward and intuitive method of visualizing DILI.

Signal amplification strategies in photoelectrochemical sensing of carcinoembryonic antigen

Early detection of cancer markers is critical for cancer diagnosis and cancer therapy since these markers may indicate cancer risk, incidence, and disease prognosis. Carcinoembryonic antigen (CEA) is a type of non-specific and broad-spectrum cancer biomarker commonly utilized for early cancer diagnosis. Moreover, it serves as an essential tool to assess the efficacy of cancer treatment and monitor tumor recurrence as well as metastasis, thus garnering significant attention for precise and sensitive CEA detection. In recent years, photoelectrochemical (PEC) techniques have emerged as prominent methods in CEA detection due to the advantages of PEC, such as simple equipment requirements, cost-effectiveness, high sensitivity, low interference from background signals, and easy of instrument miniaturization. Different signal amplification methods have been reported in PEC sensors for CEA analysis. Based on these, this article reviews PEC sensors based on various signal amplification strategies for detection of CEA during the last five years. The advantages and drawbacks of these sensors were discussed, as well as future challenges.

Spectral insights: Navigating the frontiers of biomedical and microbiological exploration with Raman spectroscopy

Raman spectroscopy (RS), a powerful analytical technique, has gained increasing recognition and utility in the fields of biomedical and biological research. Raman spectroscopic analyses find extensive application in the field of medicine and are employed for intricate research endeavors and diagnostic purposes. Consequently, it enjoys broad utilization within the realm of biological research, facilitating the identification of cellular classifications, metabolite profiling within the cellular milieu, and the assessment of pigment constituents within microalgae. This article also explores the multifaceted role of RS in these domains, highlighting its distinct advantages, acknowledging its limitations, and proposing strategies for enhancement.

Simultaneous and sensitive detection of SARS-CoV-2 proteins spike and nucleocapsid based on long-range SERS biosensor

BACKGROUND

Early diagnosis of SARS-CoV-2 infection is still critical to control COVID-19 outbreak. Traditional polymerase chain reaction, enzyme-linked immunosorbent assay or lateral flow immunoassay performed poorly on detection times, sample preparation process and accuracy. Surface-enhanced Raman scattering (SERS)-based detection has emerged as a powerful analytical technique, which overcomes the above limitations. However, due to the near-field effect of traditional substrate, it is difficult to monitor the binding event of aptamers with proteins. It is obvious that a novel SERS substrate thatsupportedextended and stronger electromagnetic fields was required to hold long-range effects and allow for binding event testing.

RESULTS

Driven by this challenge, we reported a long-range SERS-active substrate, which was built by inserting bowtie nanoaperture arrays in a refractive-index-symmetric environment and Au mirror surfaces, for SARS-CoV-2 protein binding event detection. Then, a double-π structure aptasensor was simply designed through the hybridization of spike (S) and nucleocapsid (N) proteins aptamers, and a corresponding complementary strand. This kind of double-π structure would dissociate when targets proteins S and N existed and led to the SERS responses decreased, which established the detection basis of our system. What's more, due to two Raman labels were involved, both proteins S and N can be sensed simultaneously. Our proposed method showed improved sensitivity with a low limit of detection for multiplex detection (1.6 × 10-16 g/mL for protein S and 1.0 × 10-16 g/mL for protein N) over a wide concentration range.

SIGNIFICANCE

This represents the first long-range SERS apatasensor platform for detection of S and N proteins simultaneously. Our method showed high sensitivity, selectivity, reproducibility, stability and remarkable recoveries in human in saliva and serum samples, which is particularly important for the early diagnostics of COVID as well as for future unknown coronavirus.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

Enhancing the Reliability of SERS Detection in Ampicillin Using Oriented Tetrahedral Framework Nucleic Acid Probes and a Long-Range SERS Substrate

Indirect surface-enhanced Raman scattering (SERS)-based methods are highly efficient in detecting and quantitatively analyzing trace antibiotics in complex samples. However, the poor reproducibility of indirect SERS assays caused by the diffusion and orientation changes of the probing molecules on SERS substrates still presents a significant challenge. To address this issue, this study reports the construction of a novel SERS sensing platform using tetrahedral framework nucleic acid (tFNA) as SERS probes in conjunction with a long-range SERS (LR-SERS) substrate. The tFNA was modified with sulfhydryl groups at three vertices and appended with a probing DNA at the remaining vertex, anchored on the substrate surface with a well-ordered orientation and stable coverage density, resulting in highly reproducible SERS signals. Owing to the weak SERS signal of tFNA inherited from its size being larger than the effective range of the enhancing electric field (E-field) of conventional SERS substrates, we utilized an LR-SERS substrate to enhance the signal of tFNA probes by capitalizing on its extended E-field. Correspondingly, the LR-SERS substrate demonstrated a 54-fold increase in the intensity of tFNA probes compared to the conventional substrate. Using this novel platform, we achieved a highly reliable detection of the antibiotic ampicillin with a wide linear range (10 fM to 1 nM), low detection limit (3.1 fM), small relative standard deviation (3.12%), and yielded quantitative recoveries of 97-102% for ampicillin in water, milk, and human serum samples. These findings, therefore, effectively demonstrate the achievement of highly reliable SERS detection of antibiotics using framework nucleic acids and an LR-SERS substrate.

High-sensitivity long-range surface plasmon resonance sensing assisted by gold nanoring cavity arrays and nanocavity coupling

In many of the existing refractive index (RI) sensing works, only the shape and size of plasmonic structures are usually taken into account, while the parameters of spacer layers are ignored. In this publication, we explored the long-range surface plasmon resonance (LRSPR) and Fabry-Pérot resonance coupling effects of our proposed gold nanoring cavity array/spacer layer/Au mirror/glass substrate. Both the RI sensitivity and full width at half-maximum (FWHM) values were superior than those of conventional surface plasmon resonance substrates. We discussed the tunability of the RI sensitivity through changing the RI and thickness of the spacer layer. Then, under the optimized parameter conditions of the spacer layer, the geometry parameters (including size, gap and periodicity) of gold nanoring cavity arrays were tuned to optimize the best RI sensitivity. Finally, we broke the structural symmetry of a nanoring cavity to introduce Fano resonances into our system, and a high RI sensitivity and figure-of-merit (FOM) of 695 nm per RIU (refractive index unit) and 96.5, respectively, were achieved when the breaking angle θ was 30°. This study opens up many possibilities for boosting the FOM of RI sensing by taking into account the hybridization effects of localized surface plasmon resonance, LRSPR, and Fabry-Pérot and Fano resonances.

A copper foam-based surface-enhanced Raman scattering substrate for glucose detection

Raman spectroscopy can quickly achieve non-destructive, qualitative and quantitative detection, and analysis the molecular structure of substances. Herein, a facile and low-cost method for preparation of highly sensitivity SERS substrates was implemented through the displacement reaction of copper foam immersed in AgNO₃ ethanol solution. Due to the 3D structure of copper film and homogenous displacement, the Ag-Cu substrate showed high performance SERS enhancement (1.25 × 10⁷), and the lowest detection concentration for R6G reached 10^-10 Mol/L. For glucose detection, mixed decanethiol (DT)/mercaptohexanol (MH) interlayer was used to enable glucose attach to the substrate surface, and the limit of detection reached to 1 uM/L. SERS substrate makes the Ag-Cu SERS substrate promising for biological applications.

SARS-CoV-2 proteins monitored by long-range surface plasmon field-enhanced Raman scattering with hybrid bowtie nanoaperture arrays and nanocavities

The identification of biomacromolecules by using surface-enhanced Raman scattering (SERS) remains a challenge because of the near-field effect of traditional substrates. Long-range surface plasmon resonance (LRSPR) is a special type of surface optical phenomenon that provides higher electromagnetic field enhancement and longer penetration depth than conventional surface plasmon resonance. To break the limit of SERS detection distance and obtain a SERS substrate with increased enhancement ability, a bowtie nanoaperture array was sandwiched between two symmetric dielectric environments. Then, an Au mirror was inserted to form a metal-insulator-metal configuration. Finite-difference time-domain simulations revealed that numerous hybrid modes can be provided by this novel configuration (denoted as long-range SERS [LR-SERS] substrate). In particular, the LRSPR mode can be excited and reach the maximum value through the regulation of the polarizations of the incident light and the geometrical parameters of the LR-SERS substrate. The optimized LR-SERS substrate was then applied to detect SARS-CoV-2 spike (S) and nucleocapsid (N) proteins. This substrate displayed ultralow detection limits of ∼9.2 and ∼11.3 pg mL^-1 for the S and N proteins, respectively. Moreover, with the help of principal component analysis and receiver operating characteristic methods, our fabricated sensors exhibited excellent selectivity and hold great potential for the diagnosis of SARS-CoV-2 proteins in real samples.

Long-Range SERS Detection of the SARS-CoV-2 Antigen on a Well-Ordered Gold Hexagonal Nanoplate Film

The development of an effective method for identifying severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) via direct viral protein detection is significant but challenging in combatting the COVID-19 epidemic. As a promising approach for direct detection, viral protein detection using surface-enhanced Raman scattering (SERS) is limited by the larger viral protein size compared to the effective electromagnetic field (E-field) range because only the analyte remaining within the E-field can achieve high detection sensitivity. In this study, we designed and fabricated a novel long-range SERS (LR-SERS) substrate with an Au nanoplate film/MgF2/Au mirror/glass configuration to boost the LR-SERS resulting from the extended E-field. On applying the LR-SERS to detect the SARS-CoV-2 spike protein (S protein), reagent-free detection achieved a low detection limit of 9.8 × 10-11 g mL-1 and clear discrimination from the SARS-CoV S protein. The developed technique also allows testing of the S protein in saliva with 98% sensitivity and 100% specificity.

Gold Nanoparticle-Bridge Array to Improve DNA Hybridization Efficiency of SERS Sensors

The interfacial mass transfer rate of a target has a significant impact on the sensing performance. The surface reaction forms a concentration gradient perpendicular to the surface, wherein a slow mass transfer process decreases the interfacial reaction rate. In this work, we self-assembled gold nanoparticles (AuNPs) in the gap of a SiO₂ opal array to form a AuNP-bridge array. The diffusion paths of vertical permeability and a microvortex effect provided by the AuNP-bridge array synergistically improved the target mass transfer efficiency. As a proof of concept, we used DNA hybridization efficiency as a research model, and the surface-enhanced Raman spectroscopy (SERS) signal acted as a readout index. The experimental verification and theoretical simulation show that the AuNP-bridge array exhibited rapid mass transfer and high sensitivity. The DNA hybridization efficiency of the AuNP-bridge array was 15-fold higher than that of the AuNP-planar array. We believe that AuNP-bridge arrays can be potentially applied for screening drug candidates, genetic variations, and disease biomarkers.

CRISPR/Cas12a Coupling with Magnetic Nanoparticles and Cascaded Strand Displacement Reaction for Ultrasensitive Fluorescence Determination of Exosomal miR-21

Exosomal MicroRNA-21 (miRNA-21, miR-21) is significantly up-regulated in blood samples of patients with lung cancer. Exosomal-derived miR-21 can be used as a promising biomarker for the early diagnosis of lung cancer. This paper develops a fluorescent biosensor based on the combination of magnetic nanoparticles (MNPs), cascade strand displacement reaction (CSDR) and CRISPR/Cas12a to detect the exosomal miR-21 from lung cancer. The powerful separation performance of MNPs can eliminate the potential interference of matrix and reduce the background signal, which is very beneficial for the improvement of specificity and sensitivity. The CSDR can specifically transform one miR-21 into plenty of DNA which can specifically trigger the trans-cleavage nuclease activity of Cas12a, resulting in the cleavage of ssDNA bi-labeled with fluorescent and a quencher. Under the optimized experimental conditions, the developed fluorescence biosensor exhibited high sensitivity and specificity towards the determination of exosomal-derived miR-21 with a linear range from 10 to 1 × 10⁵ fM and a low detection limit of about 0.89 fM. Most importantly, this method can be successfully applied to distinguish the exosomal miR-21 from the lung cancer patients and the healthy people.

Dynamic SPME-SERS Induced by Electric Field: Toward In Situ Monitoring of Pharmaceuticals and Personal Care Products

The core of the surface-enhanced Raman spectroscopy (SERS)-based techniques for dynamic monitoring is to realize rapid and reversible adsorption. Herein, the integration technology of electro-enhanced adsorption, solid-phase microextraction, and surface-enhanced Raman spectroscopy (EE-SPME-SERS) was developed to obtain sensitive, ultrafast, and reversible SERS response toward in situ monitoring of pharmaceuticals and personal care products (PPCPs). In the EE-SPME-SERS method, a roughened Ag fiber with Au modification (r-Ag/Au fiber) was used as the SERS substrate, SPME sorbent, and working electrode. The r-Ag/Au fiber displayed good SERS sensitivity, ultrahigh photostability, and adsorption properties. The adsorption efficiency of benzidine was 76 times accelerated in EE-SPME-SERS compared to that in static adsorption. The whole process of "sampling and detection" in EE-SPME-SERS can be finished within 1 s. Reversible adsorption and desorption can be achieved in situ by switching the direction of electric field, and the regeneration process takes only a few minutes. Simulated release of benzidine from household wastewater was in situ and dynamically monitored using this strategy. EE-SPME-SERS was proved universal for ionized PPCPs and can detect multicomponents simultaneously. In addition, EE-SPME-SERS showed very good analytical properties. Great potential of EE-SPME-SERS can be expected in environmental monitoring.

Shape- and Size-Dependent Refractive Index Sensing and SERS Performance of Gold Nanoplates

Plasmonic sensors are promising for ultrasensitive chemical and biological analysis. Gold nanoplates (Au NPLs) show unique geometrical structures with high ratios of surface to bulk atoms, which display fascinating plasmonic properties but require optimization. This study presented a systematic investigation of the influence of different parameters (shape, aspect ratio, and resonance mode) on localized surface plasmon resonance properties, refractive index (RI, n) sensitivities, and surface-enhanced Raman scattering (SERS) enhancement ability of different types of Au NPLs through finite-difference time-domain (FDTD) simulations. As a proof of concept, triangular, circular, and hexagonal Au NPLs with varying aspect ratios were fabricated via a three-step seed-mediated growth method by the experiment. Both FDTD-simulated and measured experimental results confirm that the RI sensitivities increase with the aspect ratio. Furthermore, choosing a lower order resonance mode of Au NPLs benefits higher RI sensitivities. The SERS enhancement abilities of Au NPLs also predicted to be highly dependent on the shape and aspect ratio. The triangular Au NPLs showed the highest SERS enhancement ability, while it drastically decreased for circular Au NPLs after the rounding process. The SERS enhancement ability gradually became more intense as the hexagonal Au NPLs overgrown on circular Au NPLs with increasing volumes of HAuCl₄ solution. The results are expected to help develop effective biosensors.

Surface-enhanced Raman Scattering of Au-Ag bimetallic nanopillars fabricated using surface-plasmon lithography

Arrays of gold-silver (Au-Ag) bimetallic nanopillars were fabricated by a newly developed surface-plasmon lithography (SPL) and their enhancement properties as surface-enhanced Raman scattering (SERS) substrates have been studied. We demonstrated that the SPL is a low-cost and high efficiency method for the fabrication of SERS substrates with both high sensitivity and reproducibility. The nanopillars showed a good response in the detection of methylene blue molecules at a low concentration of 1.0 × 10^-11mol· l^-1. The SERS enhancement factors (EFs) are on the orders of 10⁷and the relative standard deviation of SERS intensity is <8% over an area of 50μm × 50μm. The EFs increase fast with the height increasing from 200 to 530 nm, then increase slowly when further increase the height of the nanopillars to 1100 nm. In addition, the Au-Ag bimetallic coating has shown much higher SERS enhancement than the coatings of either the pure Au or Ag. The excellent SERS enhancement and reproducibility of the Au-Ag coated nanopillars indicated that the fabricated SERS substrates can be used for the detection of biochemical molecules at trace level and the SPL is a promising method for fabrication of SERS substrates.

The finite-difference time-domain (FDTD) guided preparation of Ag nanostructures on Ti substrate for sensitive SERS detection of small molecules

Surface-enhanced Raman Scattering (SERS) has become a powerful analytical technique for highly sensitive detection of target molecules. Its performance, however, is heavily dependent on the substrates. Relatively low sensitivity for small molecules and poor reproducibility in quantitative analysis are often encountered in most of nanoparticle modified SERS substrate. The present work starts by theoretical investigation of the electromagnetic field enhancement by nanomaterials of coinage metals with different sizes. The finite-difference time-domain (FDTD) simulation results revealed that the Ag NPs with the size around 100 nm exhibit the strongest SERS effect and the 'Ag-Ag' gaps have shown higher electromagnetic field enhancement than that of the 'Ag-Ti' gap. Subsequently, a multilayered Ag nanoparticles SERS substrate (or other coinage metals) was prepared by a two-step electroless deposition of Ag on Ti substrate. This was achieved by in situ reduction of Ag precursor to subsequently form a Ag nanoflake (Ag NF) layer and a Ag nanoparticle (Ag NPs) layer on the Ti base (Ti/AgNFs/AgNPs). The as-prepared SERS substrate showed a substantially enhanced SERS effect for small molecule detection and detection limit as low as 1.0 × 10^-17 M for picric acid (PA), 1.0 × 10^-14 M for p-nitrotoluene (PNT) and 1.0 × 10^-6 M for uric acid (UA) were obtained respectively. The facile method developed in this work should be widely applicable for in-situ preparation of other SERs substrates.

Photoactivated DNA Walker Based on DNA Nanoflares for Signal-Amplified MicroRNA Imaging in Single Living Cells

Specific and sensitive detection and imaging of cancer-related miRNA in living cells are desirable for cancer diagnosis and treatment. Because of the spatiotemporal variability of miRNA expression level during different cell cycles, signal amplification strategies that can be activated by external stimuli are required to image miRNAs on demand at desired times and selected locations. Herein, we develop a signal amplification strategy termed as the photoactivated DNA walker based on DNA nanoflares, which enables photocontrollable signal amplification imaging of cancer-related miRNA in single living cells. The developed method is achieved via combining photoactivated nucleic acid displacement reaction with the traditional exonuclease III (EXO III)-assisted DNA walker based on DNA nanoflares. This method is capable of on-demand activation of the DNA walker for dictated signal amplification imaging of cancer-related miRNA in single living cells. The developed method was demonstrated as a proof of concept to achieve photoactivated signal amplification imaging of miRNA-21 in single living HeLa cells via selective two-photon irradiation (λ = 740 nm) of single living HeLa cells by using confocal microscopy equipped with a femtosecond laser.

Traditional and new applications of the HCR in biosensing and biomedicine

The hybridization chain reaction is a very popular isothermal nucleic acid amplification technology. A single-stranded DNA initiator triggers an alternate hybridization event between two hairpins forming a double helix polymer. Due to isothermal, enzyme-free and high amplification efficiency characteristics, the HCR is often used as a signal amplification technology for various biosensing and biomedicine fields. However, as an enzyme-free self-assembly reaction, it has some inevitable shortcomings of relatively slow kinetics, low cell internalization efficiency, weak biostability of DNA probes and uncontrollable reaction in these applications. More and more researchers use this reaction system to synthesize new materials. New materials can avoid these problems skillfully by virtue of their inherent biological characteristics, molecular recognition ability, sequence programmability and biocompatibility. Here, we summarized the traditional application of the HCR in biosensing and biomedicine in recent years, and also introduced its new application in the synthesis of new materials for biosensing and biomedicine. Finally, we summarized the development and challenges of the HCR in biosensing and biomedicine in recent years. We hope to give readers some enlightenment and help.